Iron in the structure of Refined Structure of Cytochrome C3 At 1.8 Angstroms Resolution (pdb 2cdv)

The binding sites of Iron atom in the structure of Refined Structure of Cytochrome C3 At 1.8 Angstroms Resolution (pdb code 2cdv). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2cdv structure was solved by Y.HIGUCHI, M.KUSUNOKI, Y.MATSUURA, N.YASUOKA, M.KAKUDO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 1.8 Space group P212121 a (A) 52.900 b (A) 68.100 c (A) 34.900 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.6 Rfree (%) n/a Iron Binding Sites: Iron binding site 1 out of 4 in 2cdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2cdv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Tyr66, A: His70, A: His106, A: Hem108, conact list: Atom Atom Distance (A) Fe CE2 A:Tyr66 4.95 Fe NE2 A:His70 1.93 Fe ND1 A:His70 4.03 Fe CD2 A:His70 3.00 Fe CE1 A:His70 2.89 Fe CG A:His70 4.10 Fe NE2 A:His106 1.94 Fe ND1 A:His106 4.06 Fe CD2 A:His106 3.06 Fe CE1 A:His106 2.89 Fe CG A:His106 4.17 Fe C2D A:Hem108 4.28 Fe NC A:Hem108 1.99 Fe CHB A:Hem108 3.45 Fe CHC A:Hem108 3.37 Fe C3D A:Hem108 4.28 Fe NA A:Hem108 2.03 Fe CHA A:Hem108 3.44 Fe C2A A:Hem108 4.30 Fe C1D A:Hem108 3.04 Fe C4A A:Hem108 3.06 Fe C4B A:Hem108 3.04 Fe C3A A:Hem108 4.30 Fe C4C A:Hem108 3.01 Fe C2B A:Hem108 4.25 Fe C1C A:Hem108 3.02 Fe C2C A:Hem108 4.19 Fe ND A:Hem108 2.01 Fe CHD A:Hem108 3.42 Fe C1B A:Hem108 3.04 Fe NB A:Hem108 1.99 Fe FE A:Hem108 0.00 Fe C3C A:Hem108 4.23 Fe C3B A:Hem108 4.22 Fe C4D A:Hem108 3.06 Fe C1A A:Hem108 3.09 interactive model: Iron binding site 2 out of 4 in 2cdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2cdv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His35, A: His52, A: Hem109, conact list: Atom Atom Distance (A) Fe NE2 A:His35 2.06 Fe ND1 A:His35 4.12 Fe CD2 A:His35 3.10 Fe CE1 A:His35 2.98 Fe CG A:His35 4.22 Fe NE2 A:His52 2.05 Fe ND1 A:His52 4.14 Fe CD2 A:His52 3.08 Fe CE1 A:His52 3.01 Fe CG A:His52 4.20 Fe C2D A:Hem109 4.23 Fe NC A:Hem109 2.00 Fe CHB A:Hem109 3.45 Fe CHC A:Hem109 3.34 Fe C3D A:Hem109 4.23 Fe NA A:Hem109 2.04 Fe CHA A:Hem109 3.40 Fe C2A A:Hem109 4.30 Fe C1D A:Hem109 3.02 Fe C4A A:Hem109 3.09 Fe C4B A:Hem109 3.01 Fe C3A A:Hem109 4.33 Fe C4C A:Hem109 3.03 Fe C2B A:Hem109 4.23 Fe C1C A:Hem109 3.00 Fe C2C A:Hem109 4.24 Fe ND A:Hem109 1.97 Fe CHD A:Hem109 3.39 Fe C1B A:Hem109 3.04 Fe NB A:Hem109 1.98 Fe FE A:Hem109 0.00 Fe C3C A:Hem109 4.25 Fe C3B A:Hem109 4.23 Fe C4D A:Hem109 3.01 Fe C1A A:Hem109 3.06 interactive model: Iron binding site 3 out of 4 in 2cdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2cdv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Pro5, A: Phe20, A: His22, A: His34, A: Hem110, conact list: Atom Atom Distance (A) Fe CD A:Pro5 4.56 Fe CE2 A:Phe20 4.68 Fe NE2 A:His22 2.02 Fe ND1 A:His22 4.09 Fe CD2 A:His22 3.10 Fe CE1 A:His22 2.93 Fe CG A:His22 4.19 Fe NE2 A:His34 1.88 Fe ND1 A:His34 4.00 Fe CD2 A:His34 2.93 Fe CE1 A:His34 2.86 Fe CG A:His34 4.05 Fe C2D A:Hem110 4.21 Fe NC A:Hem110 1.99 Fe CHB A:Hem110 3.42 Fe CHC A:Hem110 3.36 Fe C3D A:Hem110 4.23 Fe NA A:Hem110 2.00 Fe CHA A:Hem110 3.41 Fe C2A A:Hem110 4.27 Fe C1D A:Hem110 3.00 Fe C4A A:Hem110 3.05 Fe C4B A:Hem110 3.05 Fe C3A A:Hem110 4.28 Fe C4C A:Hem110 3.05 Fe C2B A:Hem110 4.28 Fe C1C A:Hem110 3.02 Fe C2C A:Hem110 4.23 Fe ND A:Hem110 1.98 Fe CHD A:Hem110 3.39 Fe C1B A:Hem110 3.05 Fe NB A:Hem110 2.01 Fe FE A:Hem110 0.00 Fe C3C A:Hem110 4.24 Fe C3B A:Hem110 4.28 Fe C4D A:Hem110 3.02 Fe C1A A:Hem110 3.04 interactive model: Iron binding site 4 out of 4 in 2cdv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2cdv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Phe20, A: His25, A: His83, A: Hem111, conact list: Atom Atom Distance (A) Fe CE1 A:Phe20 4.97 Fe NE2 A:His25 2.12 Fe ND1 A:His25 4.27 Fe CD2 A:His25 2.92 Fe CE1 A:His25 3.27 Fe CG A:His25 4.14 Fe NE2 A:His83 1.95 Fe ND1 A:His83 3.96 Fe CD2 A:His83 3.11 Fe CE1 A:His83 2.76 Fe CG A:His83 4.14 Fe C2D A:Hem111 4.26 Fe NC A:Hem111 2.00 Fe CHB A:Hem111 3.37 Fe CHC A:Hem111 3.41 Fe C3D A:Hem111 4.25 Fe NA A:Hem111 2.00 Fe CHA A:Hem111 3.40 Fe C2A A:Hem111 4.26 Fe C1D A:Hem111 3.04 Fe C4A A:Hem111 3.04 Fe C4B A:Hem111 3.04 Fe C3A A:Hem111 4.26 Fe C4C A:Hem111 3.04 Fe C2B A:Hem111 4.26 Fe C1C A:Hem111 3.05 Fe C2C A:Hem111 4.27 Fe ND A:Hem111 2.01 Fe CHD A:Hem111 3.41 Fe C1B A:Hem111 3.04 Fe NB A:Hem111 2.01 Fe FE A:Hem111 0.00 Fe C3C A:Hem111 4.25 Fe C3B A:Hem111 4.28 Fe C4D A:Hem111 3.04 Fe C1A A:Hem111 3.04 interactive model: